xpathApply: How to pass multiple paths or nodes? - r

Question

# parse PubMed data
library(XML) # xpath
library(rentrez) # entrez_fetch
pmids <- c("25506969","25032371","24983039","24983034","24983032","24983031","26386083",
"26273372","26066373","25837167","25466451","25013473","23733758")
# Above IDs are mix of Books and journal articles
# ID# 23733758 is an journal article and has No abstract
data.pubmed <- entrez_fetch(db = "pubmed", id = pmids, rettype = "xml",
parsed = TRUE)
abstracts <- xpathApply(data.pubmed, "//Abstract", xmlValue)
names(abstracts) <- pmids
It works well if every record has an abstract. However, when there is a PMID (#23733758) without a pubmed abstract ( or a book article or something else), it skips resulting in an error 'names' attribute [5] must be the same length as the vector [4]
Q: How to pass multiple paths/nodes so that, I can extract journal article, Books or Reviews ?
UPDATE : hrbrmstr solution helps to address the NA. But,can xpathApply take multiple nodes like c(//Abstract, //ReviewArticle , etc etc )?

Answer 1

You have to attack it one tag element up:
abstracts <- xpathApply(data.pubmed, "//PubmedArticle//Article", function(x) {
val <- xpathSApply(x, "./Abstract", xmlValue)
if (length(val)==0) val <- NA_character_
val
})
names(abstracts) <- pmids
str(abstracts)
List of 5
## $ 24019382: chr "Adenocarcinoma of the lung, a leading cause of cancer death, frequently displays mutational activation of the KRAS proto-oncoge"| __truncated__
## $ 23927882: chr "Mutations in components of the mitogen-activated protein kinase (MAPK) cascade may be a new candidate for target for lung cance"| __truncated__
## $ 23825589: chr "Aberrant activation of MAP kinase signaling pathway and loss of tumor suppressor LKB1 have been implicated in lung cancer devel"| __truncated__
## $ 23792568: chr "Sorafenib, the first agent developed to target BRAF mutant melanoma, is a multi-kinase inhibitor that was approved by the FDA f"| __truncated__
## $ 23733758: chr NA
Per your comment with an alternate way to do this:
str(xpathApply(data.pubmed, '//PubmedArticle//Article', function(x) {
xmlValue(xmlChildren(x)$Abstract)
}))
## List of 5
## $ : chr "Adenocarcinoma of the lung, a leading cause of cancer death, frequently displays mutational activation of the KRAS proto-oncoge"| __truncated__
## $ : chr "Mutations in components of the mitogen-activated protein kinase (MAPK) cascade may be a new candidate for target for lung cance"| __truncated__
## $ : chr "Aberrant activation of MAP kinase signaling pathway and loss of tumor suppressor LKB1 have been implicated in lung cancer devel"| __truncated__
## $ : chr "Sorafenib, the first agent developed to target BRAF mutant melanoma, is a multi-kinase inhibitor that was approved by the FDA f"| __truncated__
## $ : chr NA